[BioC] graph::join discards node and edge attributes

[Nishant Gopalakrishnan]

Hi Paul,

The join/union/ intersect methods for the graph objects do not preserve
the edge or the node attributes. I do not think there are any plans to
add this feature the old graph classes.

However, the new graphBAM class has methods that will hopefully do what
you are looking for . The graphUnion method performs union of two graphs
while preserving the node and edge attributes.  If there is a conflict
of attributes, it is filled with NA. You do have the option of resolving
the conflict by providing a named list of functions to the edgeFun or
nodeFun arguments of the graphUnion method.
The function should
  1. take in two arguments and returns a conflict resolved value for the
attribute.
  2. have the same name as the attribute

I shall illustrate with some simple examples for the edge attributes below

### Create two  graphs g1 and g2  with color and weight edge attributes
from = c("a", "b", "d", "d")
to   = c("b", "c", "y", "x")
weight=c(1.2, 2.4, 5.4, 3.2)
df <- data.frame(from, to, weight)
g1 <- graphBAM(df, edgemode = "directed")
edgeData(g1, attr = "color") <- "green"  ## set the default
edgeData(g1, from = c("a","b"), to = c("b", "c") , attr = "color") <-
c("yellow", "blue")

from = c("a", "b", "b", "d", "d")
to   = c("b", "c", "d", "c", "x")
weight=c(1.2, 4.2, 5.6, 2.1, 3.2)
df <- data.frame(from, to, weight)
g2 <- graphBAM(df, nodes = c("a","b","c", "d", "x", "y", "z"),
    edgemode = "directed")
edgeData(g2, attr = "color") <- "green"
edgeData(g2, from =  c("a","b"), to = c("b", "c") , attr = "color") <-
c("yellow", "cyan")

## confilicting attributes are filled with NA in the result
g <- graphUnion(g1, g2)  
edgeData(g, attr = "weight")  
edgeData(g, attr = "color")

## Provide a function for resolving conflicting weight attribute, I want
the sum of
## weights in case of conflict
g <- graphUnion(g1, g2, edgeFun = list(weight = sum))
edgeData(g, attr = "weight")
edgeData(g, attr = "color")

If you wanted to resolve the conflict for the attribute color for the
edges, you could write a function
myFun <- function(x, y) {
  ## resolve conflict here
}
and pass it  an argument to the graphUnion method.
g <- graphUnion(g1, g2, edgeFun = list(weight = sum, color = myFun))

Node attributes if present are also handled in exactly the same manner.
If conflicting node attributes occur in the union process , there is
another argument  nodeFun that you can use to pass in a function for
resolving the conflict.

I hope that answers your question.

Nishant

On 11/29/2010 09:11 AM, Paul Shannon wrote:
> I have two well-annotated kegg pathway graphs I wish to merge.
>
> Using graph::join, the nodes and edges merge nicely, but all the edge and node attributes are lost, and a new edge attribute 'weight' is added.
>
>   
>> names (nodeDataDefaults (g.05200))  
>>     
>    [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
>   
>> names (nodeDataDefaults (g.04010))  
>>     
>    [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
>   
>> names (nodeDataDefaults (g.both))   
>>     
>   NULL
>
>
>   
>> names (edgeDataDefaults (g.04010))
>>     
>   [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
>   
>> names (edgeDataDefaults (g.05200))
>>     
>   [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
>   
>> names (edgeDataDefaults (g.both))
>>     
>   [1] "weight"
>
> Is there any graph method, current or planned, which will preserve node and edge attributes?  I realize that attribute conflicts can arise, and some strategy is required to handle these.
>
>  - Paul
>
>
>   
>> sessionInfo ()
>>     
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] RCytoscape_1.1.6     org.Mm.eg.db_2.4.1   RCurl_1.4-3          bitops_1.0-4.1       GOstats_2.16.0       Category_2.16.0      GO.db_2.4.5
>  [8] GSEABase_1.11.2      annotate_1.28.0      KEGG.db_2.4.1        KEGGgraph_1.4.0      graph_1.26.0         XML_3.2-0            SPIA_1.8.0
> [15] org.Hs.eg.db_2.4.6   RSQLite_0.9-2        DBI_0.2-5            AnnotationDbi_1.11.8 Biobase_2.10.0       RUnit_0.4.26
>
> loaded via a namespace (and not attached):
> [1] genefilter_1.32.0 RBGL_1.25.0       splines_2.12.0    survival_2.35-8   tools_2.12.0      XMLRPC_0.2-2      xtable_1.5-6
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>